I am treating some RNASeq data whose experimental design includes three factors. I am interested, at first, in retrieving those genes showing the triple interaction, using voom + lmFit. I’ve read several posts on the matter, but none answered my question, so much so considering that one of my factors (i.e. time) presents multiple levels, and not just two. Is there any way to get the triple interaction out of this? IF so, should I always go through the makeContrast option and not writing the model as in “~factor1*factor2*factor3”?
I paste a code here below. Any help will be much appreciated. Thanks a lot.
design.factor <- paste(rep(c("Mock","Bact"),each=30),
dge <- DGEList(counts=counts, group=design.factor)
dge <- calcNormFactors(dge)
dge.voom <- voom(dge,plot=TRUE)
fit <- lmFit (dge.voom,design)